tidied up system.out messages and moved many to stderr.

[jalview.git] / src / jalview / io / PfamFile.java

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index e17f831..3a02041 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -125,7 +125,7 @@ public class PfamFile extends AlignFile {
           throw new IOException("Not a valid protein sequence - (PFAM input)");\r
       }\r
       else\r
-        System.out.println("Can't find sequence for " + headers.elementAt(i));\r
+        System.err.println("PFAM File reader: Can't find sequence for " + headers.elementAt(i));\r
 \r
     }\r
 \r